ChIP-Seq of H3K9me3 and H3K36me3 after GFP or dKDM4A RNAi of S2 cells

Analysis of H3K9me3 and H3K36me3 levels in unique and repetitive regions of Drosophila genome after GFP (control) or dKDM4A RNAi of S2 cells After 5 days of RNAi, chromatin was prepared by fixation of 2x10^7 S2 cells with 1% paraformaldehyde for 10 minutes and shearing with Bioruptor sonicator (30 cycles). ChIP was performed by overnight incubation of chromatin with Protein-A Dynabeads and 5 ug of either anti-H3K36me3 or anti-H3K9me3 ChIP-grade antibody (Abcam). Library construction was conducted using TruSeq DNA sample preparation kit (Illumina). All sequencing data were obtained from the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley.